The advantage of bundles is that it contains more metadata than a simple tarball.
Compatibility problems might arise, but at least the application launcher could provide more
meaningful feedback to the user.
Or even integrate with the OS' version control system, especially now that Linux has
PackageKit, to say "hey, the user wants to run this new bundle that needs libfoo-x.y, install
whatever package is necessary to provide that".
You'd need a package management system that automatically scans built packages for what
libraries they provide; RPM does that, not sure whether DPKG does.